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- PDB-4mya: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase w... -

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Basic information

Entry
Database: PDB / ID: 4mya
TitleCrystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor A110
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel / alpha-beta structure / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2EY / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8997 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Gu, M. / Gorla, S.K. / Hedstrom, L. / Anderson, W.F. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the Inosine 5'-monophosphate Dehydrogenase with an Internal Deletion of the CBS Domain from Bacillus anthracis str. Ames complexed with inhibitor A110
Authors: Kim, Y. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1259
Polymers81,4192
Non-polymers1,7067
Water8,845491
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,43520
Polymers162,8384
Non-polymers3,59716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area25810 Å2
ΔGint-136 kcal/mol
Surface area46630 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,06716
Polymers162,8384
Non-polymers3,22812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area24580 Å2
ΔGint-120 kcal/mol
Surface area46880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.852, 110.852, 56.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 40709.574 Da / Num. of mol.: 2 / Fragment: IMPDH-delt-L-CBS / Mutation: replaced residues 92-220 with GG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: guaB, BA_0008, BAS0011, GBAA_0008 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81W29, UniProt: A0A6L8P2U9*PLUS, IMP dehydrogenase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-2EY / 4-{(1R)-1-[1-(4-chlorophenyl)-1H-1,2,3-triazol-4-yl]ethoxy}quinolin-2(1H)-one


Mass: 366.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15ClN4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1 M Ches pH 9.5, 10% w/v PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.8997→50 Å / Num. all: 53268 / Num. obs: 53268 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 16.82 Å2 / Rsym value: 0.099 / Net I/σ(I): 7.5
Reflection shellResolution: 1.8997→1.93 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2224 / Rsym value: 0.463 / % possible all: 81.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID ENTRY 3TSD

3tsd


Resolution: 1.8997→49.575 Å / SU ML: 0.15 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2697 5.07 %random
Rwork0.147 ---
all0.149 53247 --
obs0.149 53247 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8997→49.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5119 0 116 491 5726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075463
X-RAY DIFFRACTIONf_angle_d1.2167411
X-RAY DIFFRACTIONf_dihedral_angle_d14.0812010
X-RAY DIFFRACTIONf_chiral_restr0.071851
X-RAY DIFFRACTIONf_plane_restr0.004955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8997-1.93430.22531320.20842202233482
1.9343-1.97150.2341170.20192443256090
1.9715-2.01170.21541410.19722595273696
2.0117-2.05550.24491430.180926612804100
2.0555-2.10330.22551220.162127232845100
2.1033-2.15590.19631310.153726712802100
2.1559-2.21420.1911460.145227022848100
2.2142-2.27930.19051280.141926782806100
2.2793-2.35290.191710.143627082879100
2.3529-2.4370.19241760.1426552831100
2.437-2.53450.18791350.144727152850100
2.5345-2.64990.19121550.141426652820100
2.6499-2.78960.19921370.147727062843100
2.7896-2.96430.21031330.140227322865100
2.9643-3.19320.18861430.145726962839100
3.1932-3.51440.16171400.140927322872100
3.5144-4.02280.14511450.130627332878100
4.0228-5.06750.15891590.124427312890100
5.0675-49.59140.16761430.15562802294599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7645-1.17790.02946.328-0.99320.7363-0.0337-0.07440.06070.4052-0.043-0.21660.0047-0.00450.07650.0645-0.0196-0.0240.1138-0.00370.068210.94665.878611.6975
22.0366-0.3409-1.00442.54460.91022.32820.02850.09540.075-0.1023-0.0381-0.23150.00580.10460.01980.0678-0.01630.00840.07820.03150.11330.867918.0697-3.1051
31.30510.475-0.15161.5703-0.25810.707-0.011-0.0568-0.1073-0.0001-0.0767-0.36310.02610.16340.04940.06650.0075-0.01530.10720.02660.138832.06827.58344.2302
41.116-0.2075-0.28542.9957-1.28732.1461-0.11170.3901-0.0987-0.99450.0883-0.04930.1880.01220.00930.41-0.0364-0.00420.21710.00730.105525.03667.2413-17.5093
50.42330.1047-0.34752.4523-0.10991.22910.0370.10660.0494-0.4634-0.0095-0.2290.01420.062-0.0230.093-0.0092-0.02440.13260.01090.096621.160512.5285-8.3486
60.88330.0547-0.02391.5352-0.05551.38150.00940.4928-0.1269-0.32720.05730.1948-0.0224-0.181-0.05080.1760.0035-0.04790.2887-0.04180.15487.426617.25240.5281
71.248-1.8278-0.07296.64370.47030.7843-0.0267-0.0732-0.09580.227-0.0180.15930.00320.02770.02590.0423-0.03110.00150.09660.01310.070545.195247.8342-15.987
81.45990.50810.28251.47330.60841.4915-0.0379-0.01530.0855-0.1535-0.22350.4832-0.1111-0.31350.14770.07520.0139-0.01890.1247-0.05260.192319.762140.9393-26.9819
91.0128-0.35610.35672.59910.340.2251-0.0008-0.0663-0.01160.003-0.0572-0.0326-0.0029-0.04930.04980.052-0.00810.00530.0793-0.00870.051834.664945.59-21.971
104.4613-0.212-1.35371.8113-0.3213.15310.10691.08050.2844-1.21690.2525-0.4572-0.53850.0816-0.19190.6583-0.05950.15260.2884-0.02260.173733.407542.07-47.2423
110.55280.52420.17721.32470.70941.64120.01320.165-0.0726-0.5926-0.01950.2116-0.1839-0.14580.04510.2073-0.02060.02230.1591-0.02220.100433.824343.4483-38.1098
120.6969-0.12080.12071.35620.39461.3251-0.09810.49950.1526-0.34050.094-0.2378-0.02440.2209-0.00310.1738-0.02570.06020.32970.09150.203249.546637.5778-27.0966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 363 )
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 398 )
5X-RAY DIFFRACTION5chain 'A' and (resid 399 through 446 )
6X-RAY DIFFRACTION6chain 'A' and (resid 447 through 485 )
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 26 )
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 293 )
9X-RAY DIFFRACTION9chain 'B' and (resid 294 through 363 )
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 383 )
11X-RAY DIFFRACTION11chain 'B' and (resid 384 through 446 )
12X-RAY DIFFRACTION12chain 'B' and (resid 447 through 485 )

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